ArticleScience advances2021
Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath.
Article in Science advances, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Towards efficient perturbation for the noncoding genome.Nature communications · 2026Article
- CRISPR tiling deletion screens reveal functional enhancers and allelic compensation effects (ACE) on SIN3A transcription.Nature communications · 2026Article
- Review
- Functional phenotyping of genomic variants using joint multiomic single-cell DNA-RNA sequencing.Nature methods · 2025Article
- Chromatin interaction-based annotation of regulatory elements reveals dynamic promoter-enhancer interactions in lymphocyte development.iScience · 2025Article
- Three-dimensional regulatory hubs support oncogenic programs in glioblastoma.Molecular cell · 2025Article
- Engineered CRISPR-Cas12a for higher-order combinatorial chromatin perturbations.Nature biotechnology · 2025Article
- Dysregulated Gene Expression: A Candidate Mechanism for Anxiety Disorders.Journal of psychiatry and brain science · 2025Article
- Three-dimensional regulatory hubs support oncogenic programs in glioblastoma.bioRxiv : the preprint server for biology · 2024Article
- High-throughput PRIME-editing screens identify functional DNA variants in the human genome.Molecular cell · 2023Article
- Gene regulatory network inference in the era of single-cell multi-omics.Nature reviews. Genetics · 2023Review
- Review
- 3D enhancer-promoter interactions and multi-connected hubs: Organizational principles and functional roles.Cell reports · 2023Review
- Quantitative trait locus (xQTL) approaches identify risk genes and drug targets from human non-coding genomes.Human molecular genetics · 2022Review
- High-throughput CRISPRi and CRISPRa technologies in 3D genome regulation for neuropsychiatric diseases.Human molecular genetics · 2022Review
- Functional genomic assays to annotate enhancer-promoter interactions genome wide.Human molecular genetics · 2022Review
- HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization.Molecular cell · 2022Article
- Super interactive promoters provide insight into cell type-specific regulatory networks in blood lineage cell types.PLoS genetics · 2022Article
Corrections and comments
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Authors and funding
21 authors.
Funding
Abstract
Current pooled CRISPR screens for cis-regulatory elements (CREs), based on transcriptional output changes, are typically limited to characterizing CREs of only one gene. Here, we describe CRISPRpath, a scalable screening strategy for parallelly characterizing CREs of genes linked to the same biological pathway and converging phenotypes. We demonstrate the ability of CRISPRpath for simultaneously identifying functional enhancers of six genes in the 6-thioguanine–induced DNA mismatch repair pathway using both CRISPR interference (CRISPRi) and CRISPR nuclease (CRISPRn) approaches. Sixty percent of the identified enhancers are known promoters with distinct epigenomic features compared to other active promoters, including increased chromatin accessibility and interactivity. Furthermore, by imposing different levels of selection pressure, CRISPRpath can distinguish enhancers exerting strong impact on gene expression from those exerting weak impact. Our results offer a nuanced view of cis-regulation and demonstrate that CRISPRpath can be leveraged for understanding the complex gene regulatory program beyond transcriptional output at scale.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.